Alignments for a candidate for sdaB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Echinicola vietnamensis KMM 6221, DSM 17526

Align L-serine dehydratase, alpha chain; SDH; EC 4.3.1.17; L-serine deaminase; L-SD (uncharacterized)
to candidate Echvi_0600 Echvi_0600 L-serine dehydratase, iron-sulfur-dependent, alpha subunit

Query= curated2:P33073
         (292 letters)



>FitnessBrowser__Cola:Echvi_0600
          Length = 302

 Score =  204 bits (519), Expect = 2e-57
 Identities = 114/279 (40%), Positives = 163/279 (58%), Gaps = 3/279 (1%)

Query: 10  DVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDVTEYKMID 69
           + C  + + +Y  V+E E      +EE+I + L +   VM  +    L +  V+   MI+
Sbjct: 13  EYCEAKNVPLYAPVMEYEKDQRGKSEEQIWEGLRSAYKVMKDAVETGLKEEMVSRSGMIN 72

Query: 70  GFAKRTYEYANSGKSIVGDFLAKAMAMAFSTSEVNASMGKIVAAPTAGSSGIMPAMLVAA 129
             AK+ Y +     S++     + ++ A +  EVN+ MG++VAAPTAG+SGI+P  L   
Sbjct: 73  NGAKKVYHHP---LSVLSPEFQRLISRALAAKEVNSCMGRVVAAPTAGASGILPGTLYTL 129

Query: 130 TEKYNFDRTTIQNGFLTSIGIGQVITKYATFAGAEGGCQAECGSASAMAAAALVEMLGGT 189
            E +      +  G L   G+  +I + A+ AGA GGCQAE GSA+AMA+ A+V  LGG 
Sbjct: 130 QEIHGLSDDKVLEGLLIGAGVALIIEQNASLAGAVGGCQAETGSAAAMASGAMVYCLGGN 189

Query: 190 VEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGVINAFISADLALAGVESLVPFD 249
            +Q  +A +ITI  +LGLVCDP+AGLV+ PC  RNAS    A  SA +ALA V  ++P D
Sbjct: 190 TDQVFNAVAITIQCMLGLVCDPVAGLVEIPCVVRNASAAAIANSSAQIALADVSGVIPVD 249

Query: 250 EVVIAMGEVGNSMIEALRETGLGGLAGSKTGQKIRRDFL 288
           E V AMGE+G SM    +ET LGGLA + TG+ I +  L
Sbjct: 250 ECVEAMGEIGASMENKYKETALGGLAATLTGKGIAKKVL 288


Lambda     K      H
   0.317    0.132    0.361 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 201
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 292
Length of database: 302
Length adjustment: 26
Effective length of query: 266
Effective length of database: 276
Effective search space:    73416
Effective search space used:    73416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate Echvi_0600 Echvi_0600 (L-serine dehydratase, iron-sulfur-dependent, alpha subunit)
to HMM TIGR00718 (sdaAA: L-serine dehydratase, iron-sulfur-dependent, alpha subunit (EC 4.3.1.17))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00718.hmm
# target sequence database:        /tmp/gapView.18705.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00718  [M=300]
Accession:   TIGR00718
Description: sda_alpha: L-serine dehydratase, iron-sulfur-dependent, alpha subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                            Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    3.6e-83  265.0   7.3    4.4e-83  264.8   7.3    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0600  Echvi_0600 L-serine dehydratase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0600  Echvi_0600 L-serine dehydratase, iron-sulfur-dependent, alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.8   7.3   4.4e-83   4.4e-83       6     287 ..       9     288 ..       4     297 .. 0.96

  Alignments for each domain:
  == domain 1  score: 264.8 bits;  conditional E-value: 4.4e-83
                            TIGR00718   6 kelievtkekqikisdlvleeeikvsektkeeirkkldavldvmeaavqknl.esvvsetklidGdakklqeyi 78 
                                          +   e ++ k++ ++  v+e e ++  k++e+i + l +  +vm+ av+ +l e  vs+ ++i+  akk++++ 
  lcl|FitnessBrowser__Cola:Echvi_0600   9 QGWKEYCEAKNVPLYAPVMEYEKDQRGKSEEQIWEGLRSAYKVMKDAVETGLkEEMVSRSGMINNGAKKVYHHP 82 
                                          556688999*******************************************9999**************9876 PP

                            TIGR00718  79 rsGkslvGdllldavakavatsevnaamGkivaaptaGsaGvvpatlvavkeklnfdreqiirflltaiaiGfv 152
                                              s+  + +   +++a+a++evn++mG++vaaptaG++G++p+tl++ +e    + +++ ++ll  +++  +
  lcl|FitnessBrowser__Cola:Echvi_0600  83 L---SVLSPEFQRLISRALAAKEVNSCMGRVVAAPTAGASGILPGTLYTLQEIHGLSDDKVLEGLLIGAGVALI 153
                                          5...5667788999************************************************************ PP

                            TIGR00718 153 vakyasiaGaeGGcqaevGsasamaaaalvemlGGtveqaleaaaitlknvlGlvcdpvaGlvevpcvkrnasG 226
                                          + ++as+aGa GGcqae Gsa+ama+ a+v  lGG ++q  +a+ait++ +lGlvcdpvaGlve+pcv rnas 
  lcl|FitnessBrowser__Cola:Echvi_0600 154 IEQNASLAGAVGGCQAETGSAAAMASGAMVYCLGGNTDQVFNAVAITIQCMLGLVCDPVAGLVEIPCVVRNASA 227
                                          ************************************************************************** PP

                            TIGR00718 227 vinaliaadlalaGveslvpfdevviamykvGqsmiealretGlGGlaasktGrklekdil 287
                                          ++ a  +a++ala v   +p+de v+am+++G sm +  +et lGGlaa+ tG+ + k++l
  lcl|FitnessBrowser__Cola:Echvi_0600 228 AAIANSSAQIALADVSGVIPVDECVEAMGEIGASMENKYKETALGGLAATLTGKGIAKKVL 288
                                          **********************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (302 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.52
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources